Flair collapse stuck at "renaming isoforms using gtf" without error

[dmanahan1]

Hello,

Poking around, it seems this issue has popped up a couple times before (namely, https://github.com/BrooksLabUCSC/flair/issues/175 and https://github.com/BrooksLabUCSC/flair/issues/178). I am running flair collapse:

flair collapse -g /path/to/GRCm39.primary_assembly.genome.fa -q flair_all_corrected.bed -r /path/to/*fastq.gz --gtf /path/to/gencode.vM29.annotation.gtf

To clarify, I used the corrected .bed outputted by flair correct and inputted all my fastqs using the regular expression. And checking my standard error reveals that it remained stuck at the last step listed until my job timed out:

Writing temporary files to /tmp/tmpxtmw3b13/ Annotated ends extracted from GTF Read data extracted Single-exon genes grouped, collapsing Renaming isoforms using gtf

The previous issues linked at the start of my post were from 2021 and 2022, is there an update to the possible source of this issue? flair.py seems to have changed enough that I can't find the lines equivalent referenced in those previous tickets.

Thanks!

[dmanahan1]

I tested the installation as seen on Flair's Github repository. https://github.com/BrooksLabUCSC/flair/tree/master/test

The command

make test-collapse

also did the exact same: it stalled at "Renaming isoforms using gtf". Perhaps this means the installation was incorrect? I used

pip install flair-brookslab

[dmanahan1]

I ended up trying to re-install Flair and while the conda/conda-forge installation didn't work, I ended up setting up a conda environment using the YAML file from the latest release and this was able to run flair collapse without issue. Interestingly, the error file for flair collapse didn't have a "Renaming isoforms using gtf" step despite providing the same command as previously.

[Jeltje]

Thanks for letting us know. We're reworking Flair to not use tqdm, which tends to result in omitting STDERR and STDOUT messages. They do happen, they just don't show up.